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Improve GFF reader #4

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drbecavin opened this issue Apr 10, 2019 · 0 comments
Open

Improve GFF reader #4

drbecavin opened this issue Apr 10, 2019 · 0 comments
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@drbecavin
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Data Parsing enhancement New feature or request
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Clean Bacnet for publication

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@drbecavin
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For the moment only coding sequences, tRNA and rRNA are included.
If no CDS, exon is available the element is not included.
We should include:

  • pseudogene without CDS
  • non-coding elements = gene without CDS

Test on eukaryotes with exon, intron and specific stuff

Modify specifically:
GFFNCBIReader.addSequences(LinkedHashMap<String, ChromosomeBacteriaSequence> chromosomes,HashMap<String, ArrayList<FeatureI>> listLocusTag)
In package bacnet.reader

Specifically if only one GFF line is available per feature !
Manage both cases
@drbecavin drbecavin added enhancement New feature or request Data Parsing labels Apr 10, 2019
@drbecavin drbecavin self-assigned this Aug 5, 2019
@drbecavin drbecavin added this to To do in Clean Bacnet for publication via automation Aug 5, 2019
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Data Parsing enhancement New feature or request
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Clean Bacnet for publication
  
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@drbecavin